[GE users] Problems compiling SGE62u1 in SL4

goncalo goncalo at lip.pt
Tue Dec 23 18:27:24 GMT 2008


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Hi...

I'll post here my overall procedure to compile SGE62u1 in SL4. If you 
try to do it as i quote it, probably, you may get some errors since my 
SL4 instalation could be different from yours.  You will have to tune it 
yourself. At some point you have to install some packages which could be 
missing. I've configured "yum" to use the SL4 official repositories and 
the jpackage 5 and jpackage 7 repositories. Nevertheless, here it is:


### Compile BerkeleyDB4.7 ###

1 ) # mkdir /root/BerkeleyDB4.7; cp db-4.7.25.tar.gz; cd /root/BerkeleyDB4.7
2 ) # tar xzvf db-4.7.25.tar.gz
3 ) # ./db-4.7.25/dist/configure --enable-rpc --enable-posixmutexecs
4 ) # make; make install; export BERKELEYDB_HOME=/usr/local/BerkeleyDB.4.7


### Checkout SGE62u1 ###

1 ) # mkdir /usr/local/sge; cd /usr/local/sge
2 ) # yum install cvs
3 ) # cvs -d :pserver:guest at cvs.sunsource.net:/cvs login
4 ) # cvs -d :pserver:guest at cvs.sunsource.net:/cvs checkout -r V62u1_TAG 
gridengine

### Install necessary packages for "Scientific Linux SL Release 
40rolling (SL)"

1 ) I have compiled myself and installed 
java-1.5.0-sun-devel-1.5.0.16-1jpp and java-1.5.0-sun-1.5.0.16-1jpp
2 ) # yum install ant ant-nodeps javacc junit openssl openssl-devel db4 
db4-devel pam pam-devel xorg-x11-devel openmotif openmotif-devel 
xml-commons-jaxp-1.3-apis
3 ) # export JAVA_HOME="/usr/lib/jvm/java-1.5.0-sun-1.5.0.16"
4 ) # export JAVA_BIN="${JAVA_HOME}/bin"
5 ) # export PATH="/usr/share/java/ant/bin:${JAVA_BIN}:${PATH}"

### Change default configuration files for my setup:

1 ) # cd /usr/local/sge/gridengine/source
2 ) # ex -c '1,$ s/\-Werror/' -c 'x' -s aimk
3 ) # ex -c '1,$ s/set 
SECLIBS_STATIC.*=.*\"\$OPENSSL_HOME\/lib\/libssl\.a.*\$OPENSSL_HOME\/lib\/libcrypto\.a\"/set 
SECLIBS_STATIC = \"\-L\/usr\/lib \-lkrb5 \-lz 
\$OPENSSL_HOME\/lib\/libssl\.a \$OPENSSL_HOME\/lib\/libcrypto\.a\"/g' -c 
'x' -s aimk
3 ) # ex -c '1,$ s/set OPENSSL_SOVERSION.*=.*$/set OPENSSL_SOVERSION = 
0\.9\.7a' -c 'x' -s aimk.site
4 ) # ex -c '1,$ s/set OPENSSL_HOME.*=.*$/set OPENSSL_HOME = \/usr/' -c 
'x' -s aimk.site
5 ) # ex -c '1,$ s/set BERKELEYDB_HOME.*=.*$/set BERKELEYDB_HOME = 
\/usr\/local\/BerkeleyDB\.4\.7' -c 'x' -s aimk.site
6 ) # ex -c '1,$ s/set KRB_HOME.*=.*$/set KRB_HOME = \/usr/' -c 'x' -s 
aimk.site
7 ) # ex -c '1,$ s/set INSURE4_LIBDIR.*=.*$/set INSURE4_LIBDIR = /' -c 
'x' -s aimk.site
8 ) # ex -c '1,$ s/set MAN2HTMLPATH.*=.*$/set MAN2HTMLPATH = 
\/usr\/bin/' -c 'x' -s aimk.site
9 ) # ex -c '1,$ s/set GROFFPATH.*=.*$/set GROFFPATH = \/usr\/bin/' -c 
'x' -s aimk.site
11) # ex -c '1,$ s/set SWIG.*=.*$/set SWIG = \/usr\/bin/' -c 'x' -s 
aimk.site
12) # ex -c '1,$ s/set PERL.*=.*$/set PERL = \/usr\/bin\/perl/' -c 'x' 
-s aimk.site
13) # ex -c '1,$ s/set TCLSH.*=.*$/set TCLSH = \/usr\/bin\/tclsh/' -c 
'x' -s aimk.site
14) # ex -c '1,$ s/set COPYRIGHT_DIR.*=.*$/set COPYRIGHT_DIR = 
\/usr\/local\/sge\/gridengine\/source\/sun_license/' -c 'x' -s aimk.site
15) # ex -c '1,$ s/set SUN_COPYRIGHT_DIR.*=.*$/set SUN_COPYRIGHT_DIR = 
\/usr\/local\/sge\/gridengine\/source\/sun_license/' -c 'x' -s aimk.site
16) # Substitute <arg line="@{args}"/> by <arg line="-no-dump @{args}"/> 
in /usr/local/sge/gridengine/source/libs/jgdi/build.xml
17) # ln -s /usr/bin/javacc /usr/share/java/javacc
18) # cp build.properties build_private.properties
19) # ex -c '1,$ s/javacc\.home=.*$/javacc.home=\/usr\/share\/java\/' -c 
'x' -s build_private.properties
20) # ex -c '1,$ 
s/libs\.junit\.classpath=.*$/libs\.junit\.classpath=\/usr\/share\/java\/junit.jar/' 
-c 'x' -s build_private.properties
21) # ex -c '1,$ s/OPENSSLSOVERSION=.*$/OPENSSLSOVERSION=0\.9\.7a/' -c 
'x' -s scripts/distinst.site
22) # ex -c '1,$ s/OPENSSLBASE=.*$/OPENSSLBASE=\/usr/' -c 'x' -s 
scripts/distinst.site
23) # ex -c '1,$ 
s/BERKELEYDBBASE=.*$/BERKELEYDBBASE=\/usr\/local\/BerkeleyDB\.4\.7' -c 
'x' -s scripts/distinst.site
24) # ex -c '1,$ 
s/BERKELEYDB_SHARED_LIBRARIES="libdb\-4\.4/BERKELEYDB_SHARED_LIBRARIES="libdb\-4\.7/' 
-c 'x' -s scripts/distinst
25) # ex -c '1,$ 
s/libname="\$lib\.\$shlibext\.\$OPENSSLSOVERSION"/libname="\/lib\/\$lib\.\$shlibext\.0\.9\.7a"/' 
-c 'x' -s scripts/distinst

### Compile SGE62u1

40) # ./aimk -no-dump -only-depend; ./scripts/zerodepend; ./aimk 
-no-dump depend; ./aimk -no-dump; ./aimk -no-dump -man
41) # ./scripts/distinst -allall -basedir /usr/local/sge -vdir V61u2 
lx26-x86

goncalo wrote:
> Hi All...
>
> I've been trying to compile SGE62u1 in SL4 without many success and I 
> need some help. It is not the first time I'm doing this. Indeed, I just 
> checked that my previous instructions to compile SGE61u3 still work fine 
> in the same machine, but something is now different in SGE62u1. If you 
> are not able to answer, please redirect me to somone who can help me, 
> because I already spent a lot of time in this. Here are my problems:
>
> 1) My first compilation failed with the message:
>
> [root at ui02 source]# ./aimk -no-dump -no-java
> (...)
> gcc -O3 -Wall -Werror -Wstrict-prototypes -D__GRIDENGINE_FD_SETSIZE=8192 
> -DLINUX -DLINUX86 -DLINUX86_26 -D_GNU_SOURCE -DGETHOSTBYNAME_R6 
> -DGETHOSTBYADDR_R8  -DHAS_IN_PORT_T -DLOAD_OPENSSL 
> -I/usr/local/BerkeleyDB.4.2/include/ -DSGE_ARCH_STRING=lx26-x86 
> -DTARGET_32BIT  -DSPOOLING_dynamic -DSECURE -I/usr/include 
> -Wno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DCOMPILE_DC 
> -D__SGE_COMPILE_WITH_GETTEXT__  -D__SGE_NO_USERMAPPING__ -I../common 
> -I../libs -I../libs/uti -I../libs/juti -I../libs/gdi -I../libs/japi 
> -I../libs/sgeobj -I../libs/cull -I../libs/rmon -I../libs/comm 
> -I../libs/comm/lists -I../libs/sched -I../libs/evc -I../libs/evm 
> -I../libs/mir -I../libs/lck -I../daemons/common -I../daemons/qmaster 
> -I../daemons/execd -I../daemons/schedd -I../clients/common -I. 
> -I/usr/java/latest/include -I/usr/java/latest/include/linux 
> -Wno-strict-prototypes -fPIC -ULOAD_OPENSSL -c 
> ../libs/comm/cl_ssl_framework.c -o cl_ssl_framework_static.o
> ../libs/comm/cl_ssl_framework.c: In function 
> `cl_com_ssl_build_symbol_table':
> ../libs/comm/cl_ssl_framework.c:1861: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1883: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1884: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1885: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1886: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1887: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1890: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1893: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1896: warning: assignment from 
> incompatible pointer type
> ../libs/comm/cl_ssl_framework.c:1897: warning: assignment from 
> incompatible pointer type
> make: *** [cl_ssl_framework_static.o] Error 1
> not done
>
> Something is not OK with openssl. These are the openssl packages I'm using:
>
> [root at ui02 source]# rpm -qa | grep openssl
> openssl-devel-0.9.7a-43.17.el4_6.1
> xmlsec1-openssl-1.2.6-3
> openssl-0.9.7a-43.17.el4_6.1
>
> I checked that a compilation with  "./aimk -no-dump -no-java -no-secure" 
> indeed works. Nevertheless, I DO WANT to compile with OPENSSL support.
> After searching a while, I saw that someone suggested to remove the 
> "-Werror" option in aimk. I don't know why I I'm suppose to do it since 
> before it wasn't needed and I'm using gcc 3.4.6.
>
> [root at ui02 source]# gcc -v
> Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man 
> --infodir=/usr/share/info --enable-shared --enable-threads=posix 
> --disable-checking --with-system-zlib --enable-__cxa_atexit 
> --disable-libunwind-exceptions --enable-java-awt=gtk 
> --host=i386-redhat-linux
> Thread model: posix
> gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)
>
> ---*--
>
> 2) The compilation without the "-Werror" switch in aimk also failed with:
> (...)
> [root at ui02 source]# ./aimk -no-dump -no-java
> gcc -I../daemons/shepherd -O3 -Wall  -Wstrict-prototypes 
> -D__GRIDENGINE_FD_SETSIZE=8192 -DLINUX -DLINUX86 -DLINUX86_26 
> -D_GNU_SOURCE -DGETHOSTBYNAME_R6 -DGETHOSTBYADDR_R8  -DHAS_IN_PORT_T 
> -DLOAD_OPENSSL -I/usr/local/BerkeleyDB.4.2/include/ 
> -DSGE_ARCH_STRING=lx26-x86 -DTARGET_32BIT  -DSPOOLING_berkeleydb 
> -DSECURE -I/usr/include -Wno-strict-aliasing -D_FILE_OFFSET_BITS=64 
> -DCOMPILE_DC -D__SGE_COMPILE_WITH_GETTEXT__  -D__SGE_NO_USERMAPPING__ 
> -I../common -I../libs -I../libs/uti -I../libs/juti -I../libs/gdi 
> -I../libs/japi -I../libs/sgeobj -I../libs/cull -I../libs/rmon 
> -I../libs/comm -I../libs/comm/lists -I../libs/sched -I../libs/evc 
> -I../libs/evm -I../libs/mir -I../libs/lck -I../daemons/common 
> -I../daemons/qmaster -I../daemons/execd -I../daemons/schedd 
> -I../clients/common -I. -I/usr/java/latest/include 
> -I/usr/java/latest/include/linux -L/usr/local/BerkeleyDB.4.2/lib/ -L. 
> -Wl,-rpath,\$ORIGIN/../../lib/lx26-x86 -L/usr/lib -o sge_shepherd 
> shepherd.o builtin_starter.o setrlimits.o signal_queue.o sge_shepconf.o 
> setjoblimit.o sge_pset.o sge_fileio.o sge_shepherd_ijs.o sge_ijs_comm.o 
> sge_ijs_threads.o config_file.o err_trace.o execution_states.o 
> qlogin_starter.o setosjobid.o sge_parse_num_par.o pdc.o procfs.o 
> sge_mt_init.o sge_processes_irix.o  -lgdi -lsgeobj -lsgeobjd  -lcull 
> -lcomm_static -lcommlists -luti  -llck -lrmon -ldl /usr/lib/libssl.a 
> /usr/lib/libcrypto.a  -lm -lpthread
> /usr/lib/libssl.a(kssl.o)(.text+0x170): In function 
> `populate_cksumlens':: undefined reference to `valid_cksumtype'
> /usr/lib/libssl.a(kssl.o)(.text+0x18b): In function 
> `populate_cksumlens':: undefined reference to `krb5_checksum_size'
> (...)
> /usr/lib/libssl.a(kssl.o)(.text+0x1e1b): In function 
> `kssl_validate_times':: undefined reference to `krb5_free_context'
> collect2: ld returned 1 exit status
> make: *** [sge_shepherd] Error 1
> not done
>
> I'm more or less stuck here...
>
> Cheers
> Gon?alo
>
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